An apparatus for processing a query in a plurality of heterogeneous sensor networks includes a query queue, a query combining and converting unit, a query command manager, and a data combiner. The query queue receives a plurality of queries from a user interface and stores them and the query combining and converting unit combines or converts the queries according to the heterogeneous sensor networks. The query command manager transmits the combined or converted queries to a corresponding sensor network from among the heterogeneous sensor networks, and the data combiner transmits a result according to the data received from the heterogeneous sensor networks to a user interface.